Add LES for the scalar

[timofeymukha]

Cherry pick from stress_formulation.

• Changes the scalar residual routine to accept a field for lambda
• Adds a lambda_field and nut_field_name components to the scalar_scheme.
• Adds an update_material_properties routine for the scalar_scheme, which, when the nut field (and $Pr_t$) is specified, computes the total diffusivity as

$$\rho c_p \nu_t / Pr_t + \lambda$$

• Adds documentation for this setup for the scalar setup.

@Shiyu-Sandy-Du @muenschm Note that this inverts the relationship between the solvers and the les_simcomp compared to what we had on the stress_formulation branch before. Before, the les_simcomp went into the fluid and scalar types to manipulate the lambda. Now, the scalar instead takes nut from the registry and fixes its own lambda. A similar change will follow for the fluid soon. This approach is much more future-proof.

[timofeymukha]

@timfelle What does the Make depend stage check? And what should I do to make it happy :-)?

[timfelle]

@timfelle What does the Make depend stage check? And what should I do to make it happy :-)?

Well it checks if you updated .depend. It runs makedepf90 on the repository and does a git diff to see if the .depend file changed.

Just run makedepf90 on your branch before pushing the changes.

Git diff of .depend

``` diff --git a/src/.depends b/src/.depends index c2fa887e8c..43a8627822 100644 --- a/src/.depends +++ b/src/.depends @@ -241,8 +241,8 @@ bc/bcknd/device/device_facet_normal.o : bc/bcknd/device/device_facet_normal.F90 bc/bcknd/device/device_inhom_dirichlet.o : bc/bcknd/device/device_inhom_dirichlet.F90 common/utils.o config/num_types.o bc/bcknd/device/device_dong_outflow.o : bc/bcknd/device/device_dong_outflow.F90 common/utils.o config/num_types.o scalar/bcknd/device/scalar_residual_device.o : scalar/bcknd/device/scalar_residual_device.F90 math/bcknd/device/device_mathops.o math/bcknd/device/device_math.o math/operators.o gs/gather_scatter.o scalar/scalar_residual.o -scalar/scalar_scheme.o : scalar/scalar_scheme.f90 common/time_step_controller.o field/field_series.o math/math.o scalar/scalar_source_term.o comm/comm.o common/utils.o common/material_properties.o common/user_intf.o common/json_utils.o bc/usr_scalar.o field/field_registry.o common/log.o time_schemes/time_scheme_controller.o mesh/facet_zone.o mesh/mesh.o bc/field_dirichlet.o bc/bc.o krylov/precon.o krylov/precon_fctry.o krylov/pc_hsmg.o krylov/bcknd/sx/pc_jacobi_sx.o krylov/bcknd/device/pc_jacobi_device.o krylov/bcknd/cpu/pc_jacobi.o krylov/krylov_fctry.o bc/neumann.o bc/dirichlet.o sem/coef.o krylov/krylov.o sem/dofmap.o sem/space.o field/field_list.o field/field.o config/num_types.o common/checkpoint.o gs/gather_scatter.o -scalar/scalar_pnpn.o : scalar/scalar_pnpn.f90 common/time_step_controller.o config/neko_config.o common/material_properties.o common/user_intf.o common/json_utils.o common/profiler.o fluid/advection_fctry.o fluid/advection.o common/log.o math/math.o common/projection.o time_schemes/time_scheme_controller.o scalar/scalar_aux.o math/bcknd/device/device_math.o krylov/krylov.o bc/facet_normal.o field/field_series.o math/ax.o scalar/scalar_residual.o gs/gather_scatter.o device/device.o sem/coef.o common/checkpoint.o mesh/mesh.o bc/bc.o field/field.o bc/neumann.o bc/dirichlet.o scalar/scalar_scheme.o common/rhs_maker.o common/rhs_maker_fctry.o math/ax_helm_fctry.o scalar/scalar_residual_fctry.o config/num_types.o +scalar/scalar_scheme.o : scalar/scalar_scheme.f90 common/time_step_controller.o field/field_series.o config/neko_config.o math/bcknd/device/device_math.o math/math.o scalar/scalar_source_term.o comm/comm.o common/utils.o common/material_properties.o common/user_intf.o common/json_utils.o bc/usr_scalar.o field/field_registry.o common/log.o time_schemes/time_scheme_controller.o mesh/facet_zone.o mesh/mesh.o bc/field_dirichlet.o bc/bc.o krylov/precon.o krylov/precon_fctry.o krylov/pc_hsmg.o krylov/bcknd/sx/pc_jacobi_sx.o krylov/bcknd/device/pc_jacobi_device.o krylov/bcknd/cpu/pc_jacobi.o krylov/krylov_fctry.o bc/neumann.o bc/dirichlet.o sem/coef.o krylov/krylov.o sem/dofmap.o sem/space.o field/field_list.o field/field.o config/num_types.o common/checkpoint.o gs/gather_scatter.o +scalar/scalar_pnpn.o : scalar/scalar_pnpn.f90 field/scratch_registry.o common/time_step_controller.o config/neko_config.o common/material_properties.o common/user_intf.o common/json_utils.o common/profiler.o fluid/advection_fctry.o fluid/advection.o common/log.o math/math.o common/projection.o time_schemes/time_scheme_controller.o scalar/scalar_aux.o math/bcknd/device/device_math.o krylov/krylov.o bc/facet_normal.o field/field_series.o math/ax.o scalar/scalar_residual.o gs/gather_scatter.o device/device.o sem/coef.o common/checkpoint.o mesh/mesh.o bc/bc.o field/field.o bc/neumann.o bc/dirichlet.o scalar/scalar_scheme.o common/rhs_maker.o common/rhs_maker_fctry.o math/ax_helm_fctry.o scalar/scalar_residual_fctry.o config/num_types.o scalar/scalar_aux.o : scalar/scalar_aux.f90 krylov/krylov.o config/num_types.o common/log.o scalar/scalar_residual.o : scalar/scalar_residual.f90 config/num_types.o mesh/mesh.o sem/space.o bc/facet_normal.o scalar/source_scalar.o sem/coef.o field/field.o math/ax.o gs/gather_scatter.o scalar/scalar_residual_fctry.o : scalar/scalar_residual_fctry.f90 scalar/bcknd/sx/scalar_residual_sx.o scalar/bcknd/cpu/scalar_residual_cpu.o scalar/bcknd/device/scalar_residual_device.o scalar/scalar_residual.o config/neko_config.o ```

[timofeymukha]

Ready for review now.